RegulonDB RegulonDB 11.1: Gene Form
   

tomB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

acrB tomB hha BasR PdhR CpxR TSS_622 TSS_622 TSS_621 TSS_621 TSS_620 TSS_620 TSS_619 TSS_619 TSS_618 TSS_618 TSS_617 TSS_617 TSS_616 TSS_616 tomBp tomBp hhap6 hhap6 TSS_615 (cluster) TSS_615 (cluster) TSS_614 TSS_614 TSS_613 TSS_613

Gene      
Name: tomB    Texpresso search in the literature
Synonym(s): ECK0455, EG12429, b0461, ybaJ
Genome position(nucleotides): 480334 <-- 480708
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 40.53
External database links:  
ASAP:
 ABE-0001596
ECHOBASE:
 EB2326
ECOLIHUB:
 tomB
OU-MICROARRAY:
 b0461
STRING:
 511145.b0461
COLOMBOS: tomB


Product      
Name: Hha toxicity modulator TomB
Synonym(s): TomB, YbaJ
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 14.557
Isoelectric point: 4.736
Motif(s):
 
Type Positions Sequence Comment
1 -> 117 MDEYSPKRHDIAQLKFLCETLYHDCLANLEESNHGWVNDPTSAINLQLNELIEHIATFALNYKIKYNEDNKLIEQIDEYLDDTFMLFSSYGINMQDLQKWRKSGNRLFRCFVNATKE

 
Classification:
Multifun Terms (GenProtEC)  
  5 - cell processes
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
molecular_function GO:0003677 - DNA binding
biological_process GO:0044010 - single-species biofilm formation
Note(s): Note(s): ...[more].
Evidence: [EXP-IGI] Inferred from genetic interaction
Reference(s): [1] Garcia-Contreras R., et al., 2008
External database links:  
ALPHAFOLD:
 P0AAR0
DIP:
 DIP-48132N
ECOCYC:
 EG12429-MONOMER
ECOLIWIKI:
 b0461
INTERPRO:
 IPR019693
PFAM:
 PF10757
PRIDE:
 P0AAR0
REFSEQ:
 NP_414994
SMR:
 P0AAR0
UNIPROT:
 P0AAR0


Operon      
Name: tomB-hha         
Operon arrangement:
Transcription unit        Promoter
tomB-hha


Transcriptional Regulation      
Display Regulation             
Activated by: CpxR, BasR
Repressed by: PdhR


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter TSS_613 480423 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_614 480431 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_615 (cluster) 480436 reverse nd [RS-EPT-CBR] [2]
  promoter hhap6 480503 reverse nd [COMP-AINF] [3]
  promoter TSS_616 480795 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_617 482380 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_618 482514 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_619 482517 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_620 482528 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_621 483377 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_622 483477 reverse nd [RS-EPT-CBR] [2]


Evidence    

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

 [COMP-AINF] Inferred computationally without human oversight


Reference(s)    

 [1] Garcia-Contreras R., Zhang XS., Kim Y., Wood TK., 2008, Protein translation and cell death: the role of rare tRNAs in biofilm formation and in activating dormant phage killer genes., PLoS ONE 3(6):e2394

 [2] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [3] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

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